After looking at the route the ship took it fits in with its said destiation to Bejaia, Algeria. So if there were missiles or whatever on board then they would have had to then transport them from that ship to another bound for Iran. Very hard to do if you were hiding missiles. Or the cargo was'nt missiles at all but something smaller like a batch of enriched uranium for example.

So lets just say there was something on that ship that was bound for Iran that the Russians could'nt let anyone find out about.

This is what i think happened.

The Russians got wind that a security service knew about the ships cargo. Be it isreali, American, British whoever.

They dispatched a group of spetsnaz (Russian special forces) to sieze the ship masquerading as hijackers or pirates. Steer it off course to buy them enough time to remove the cargo.

The crew would have been unaware that these men were Russian special forces and so would have acted as though they were bieng hijacked.

Then when the job was done. The official Russian forces that found the ship move in. Arresting what they believe to be pirates or hijackers and so completing the cover up.

If this is the case then the Russians would have put gagging orders on the crew and those involved in finding the ship. As they did, because anyone trained to spot Spetnaz techniques and tactics would have been able to ask the right questions in order to deduce who they really were.

So to summarise. Yes i think the russians were transporting something dodgy on that ship but no i dont believe it was missiles but something smaller but just as contraversial.